September 30, 2019

Monday morning digest covers exciting updates in microbiome with – meta analysis on role of probiotics in human depression , stool banking guidelines for fecal microbiota transplant, expert view on translation of gut microbiome to clinics and a historical peek into use of ceramic baby milk bottles in prehistoric times. Enjoy reading!

General microbiome

Translating the gut microbiome: ready for the clinic? – Susan V. Lynch – Nature Reviews Gatroenterology and Hepatology

Uterine immunity and microbiota: A shifting paradigm – Chiara Agostinis – Frontiers in Immunology

Human microbiome

Cigarette smoking and oral microbiota in low-income and African-American populations – Yaohua Yang – Journal of Epidemiology and Community Health

International consensus conference on stool banking for faecal microbiota transplantation in clinical practice – Giovanni Cammarota – Gut

Animal experiments

The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3 – Zheng Kuang – Science

Transfusional iron overload and intravenous iron infusions modify the mouse gut microbiota similarly to dietary iron – Francesca La Carpia – Biofilms and Microbiomes

Proteome modifications of gut microbiota in mice with activity-based anorexia and starvation: Role in ATP production – Jonathan Breton – Nutrition

Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut – Ulla Hynönen – Anaerobe

Intestinal inflammation increases convulsant activity and reduces antiepileptic drug efficacy in a mouse model of epilepsy – Carmen De Caro – Scientific Reports

The fecal resistome of dairy cattle is associated with diet during nursing – Jinxin Liu – Nature Communications

Neohesperidin Prevents Colorectal Tumorigenesis by Altering the Gut Microbiota – Yanling Gong – Pharmacological Research

Changes of serum lipopolysaccharide, inflammatory factors, and cecal microbiota in obese rats with type 2 diabetes induced by Roux-en-Y gastric bypass – Jiao Wu – Nutrition

Plant, root, soil microbiome

A bioinformatics guide to plant microbiome analysis – Rares Lucaciu – Frontiers in Plant Science

Beyond pathogens: microbiota interactions with the plant immune system – Paulo José PL Teixeira – Current Opinion in Microbiology

Water microbiome

Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea‐land transition – Esther Molina-Menor – Microbial Biotechnology

Probiotics

Bacillus coagulans R11 maintained intestinal villus health and decreased intestinal injury in lead-exposed mice by regulating the intestinal microbiota and influenced the function of faecal microRNAs – Si-Cheng Xing – Environmental Pollution

Effect of probiotics on depressive symptoms: A meta-analysis of human studies – Kah Kheng Goh – Psychiatry Research

Non Microbiology Picks

Milk of ruminants in ceramic baby bottles from prehistoric child graves – J. Dunne – Nature

 

September 24, 2019

Today’s digest is about diet-microbiota interactions in personalized  nutrition, interesting story on single bacterium association with fatty liver disease and how the gut microbiota adapt to red meat consumption.

General microbiome

Diet–microbiota interactions and personalized nutrition – Aleksandra A. Kolodziejczyk – Nature Reviews Microbiology

Citrobacter rodentium–host–microbiota interactions: immunity, bioenergetics and metabolism – Caroline Mullineaux-Sanders – Nature Reviews Microbiology

The interaction between the gut Microbiota and herbal medicines – Xuedong An – Biomedicine & Pharmacotherapy

Gut microbiota: what is its place in pharmacology? – Aleksandra Tarasiuk – Expert Review of Clinical Pharmacology

Human microbiome

Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae – Jing Yuan – Cell Metabolism

Association of Alterations in Intestinal Microbiota With Impaired Psychological Function in Patients With Inflammatory Bowel Diseases in Remission – Fabienne Humbel – Clinical Gastroenterology and Hepatology

Butyrate‐Producing Gut Bacteria and Viral Infections in Kidney Transplant Recipients: A Pilot Study – John R. Lee – Transplant Infectious Disease

Metabolomics and Microbial Composition Increase Insight into the Impact of Dietary Differences in Cirrhosis – I. Jane Cox – Liver International

Animal experiments

Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates – Livia S. Zaramela – Nature Microbiology

A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota – Weijun Wang – Scientific Reports

Comparative analysis of the fecal microbiota from different species of domesticated and wild suids – Florencia Correa-Fiz – Scientific Reports

Escherichia coli clonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing – Sofiya G. Shevchenko- Applied and Environmental Microbiology

Saponins from Clematis mandshurica Rupr. regulates gut microbiota and its metabolites during alleviation of collagen-induced arthritis in rats – Lin-Xiu Guo – Pharamacological Research

MHC Class II Antigen Presentation by the Intestinal Epithelium Initiates Graft-versus-Host Disease and Is Influenced by the Microbiota – Motoko Koyama – Immunity

Metformin Alters the Duodenal Microbiome and Decreases the Incidence of Pancreatic Ductal Adenocarcinoma Promoted by Diet-induced Obesity – Tien S Dong – American Journal of Physiology

Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: A multiomics approach – Maria Guirro – PlosOne

Short-chain fatty acids and microbiota metabolites attenuate ghrelin receptor signaling – Cristina Torres-Fuentes – Faseb Journal

Effects of berberine and metformin on intestinal inflammation and gut microbiome composition in db/db mice – Wang Zhang – Biomedicine & Pharmacotherapy

Plant, root, soil microbiome

Water-soluble mercury induced by organic amendments affected microbial community assemblage in mercury-polluted paddy soil – Hualing Hu – Chemosphere

Phyllosphere colonisation by a soil Streptomyces sp. promotes plant defense responses against fungal infection – Sophie Vergnes – Molecular Plant-Microbe Interactions

Water microbiome 

Heat‐induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea – Wirulda Pootakham – Microbiology Open

Probiotics
Metabolomic profiling of oxalate-degrading probiotic Lactobacillus acidophilus and Lactobacillus gasseri – Casey A. Chamberlain – PlosOne

Probiotic Bifidobacterium bifidum G9‐1 ameliorates phytohemagglutinin‐induced diarrhea caused by intestinal dysbiosis -Yutaka Makizaki – Microbiology and Immunology

May 31, 2019

Happy Friday!! Today’s digest contains reviews on the role of microbiota in immune memory formation and bioinformatic tools for soil microbiome analysis

General microbiome

*Review: The microbiome and immune memory formation – Kathy D. McCoy – Immunology and Cell biology

Preprint – Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing – Emily Crawford – bioRxiv

Animal experiments

Response of Fish Gut Microbiota to Toxin-Containing Cyanobacterial Extracts: A Microcosm Study on the Medaka (Oryzias latipes) – Sébastien Duperron – Environmental Science & Technology Letters

Plant, root, and soil microbiome

*Book chapter : Bioinformatics Tools for Soil Microbiome Analysis – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

Book chapter: Belowground Microbial Communities: Key Players for Soil and Environmental Sustainability – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

Book chapter: Single-Cell Genomics and Metagenomics for Microbial Diversity Analysis – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

In vitro digestion and fermentation of three polysaccharide fractions from Laminaria japonica and their impact on lipid metabolism-associated human gut microbiota – Jie Gao – Journal of Agricultural and Food Chemistry

Preprint – Biogeographical patterns in soil bacterial communities across the Arctic region – Lucie A Malard – bioRxiv

Water and extremophile microbiome

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient – Marie Simonin – Environmental Microbiology

Phages and viruses

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages – Jakub Barylski – Systematic Biology

Techniques

Protocol: Analysis of Microbial Siderophores by Mass Spectrometry – Tomas Pluhacek – Part of the Methods in Molecular Biology

Review: A guide to visualizing the spatial epigenome with super‐resolution microscopy – Jianquan Xu – The FEBS Journal

March 14, 2019

Today’s digest covers interesting reviews on microbiota for immunotherapies, non-digestible carbohydrates for infant microbiota and contribution of marine microbiota in reactive oxygen species; research articles on how gluten sensitivity is affected by duodenal microbiota and how ginger intake affects mouse microbiota.

General microbiome

Review: Mining the microbiota for microbial and metabolite-based immunotherapies – Ashwin N. Skelly – Nature Reviews Immunology

Pregnancy and early life microbiome

Relationship between vitamin D status and the vaginal microbiome during pregnancy – Kimberly K. Jefferson – Journal of Perinatology

Review: Shaping the Infant Microbiome With Non-Digestible Carbohydrates – Stella A. Verkhnyatskaya – Frontiers in Microbiology

Variations in early gut microbiome are associated with childhood eczema – Yu Zhang – FEMS Microbiology Letters

Human gut microbiome

Gut microbiota in HIV–pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction – Meera K. Shenoy – Microbiome

Effects of bowel preparation on the human gut microbiome and metabolome – Naoyoshi Nagata – Scientific Reports

Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic – Sarah Tomkovich – The Journal of Clinical Investigation

Animal experiments

Host NLRP6 exacerbates graft-versus-host disease independent of gut microbial composition – Tomomi Toubai – Nature Microbiology

Duodenal bacterial proteolytic activity determines sensitivity to dietary antigen through protease-activated receptor-2 – Alberto Caminero – Nature Communications

The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline – Mahdi Ghanbari – Scientific Reports

Beneficial effects of ginger on prevention of obesity through modulation of gut microbiota in mice – Jing Wang – European Journal of Nutrition

Six‐Week High‐Fat Diet Alters the Gut Microbiome and Promotes Cecal Inflammation, Endotoxin Production, and Simple Steatosis without Obesity in Male Rats – Melisa Crawford – Lipids

Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders – Elisabetta Mondo – BioRxiv

The gut microbiota regulates mouse biliary regenerative responses – Wenli Liu – BioRxiv

Plant, root, soil microbiome

Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems – Maria J. Mosqueira – Scientific Reports

Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments – Adam J. Kessler – Nature Microbiology

Effects of graphene oxide and graphite on soil bacterial and fungal diversity – Christian Forstner – BioRxiv

Water microbiome and extremophiles

Review: The microbial contribution to reactive oxygen species dynamics in marine ecosystems – Erik R. Zinser – Environmental Microbiology Reports

Non-microbiology picks

Nano-bot can probe inside human cells – Science Daily

February 27, 2019

Today’s short digest covers articles on bacterial interaction with intestinal cells, semen microbiome and how microbiota affects insulin reactive immune cells.

General microbiome

The founder hypothesis: A basis for microbiota resistance, diversity in taxa carriage, and colonization resistance against pathogens – Yael Litvak -Plos Pathogens

Review : Impact of the gut microbiome on the genome and epigenome of colon epithelial cells: contributions to colorectal cancer development – Jawara Allen – Genome Medicine

Paneth cell granule dynamics on secretory responses to bacterial stimuli in enteroids – Yuki Yokoi – Scientific Reports

Human gut microbiome

Altered immunity and microbial dysbiosis in aged individuals with long-term controlled HIV infection – Nicholas S. Rhoades – Frontiers in Immunology

Bacterial viability in faecal transplants: Which bacteria survive? – Lito E. Papanicolas – EbioMedicine

Semen Microbiome Biogeography: An Analysis Based on a Chinese Population Study – Zhanshan Ma – Frontiers in Microbiology

Animal experiments

The effects of unfermented and fermented cow and sheep milk on the gut microbiota – Elizabeth Rettedal – Frontiers in Microbiology

Altered Gut Microbiota Activate and Expand Insulin B15-23-Reactive CD8+ T-Cells – James A. Pearson – Diabetes

Lactobacillus plantarum PFM 105 Promotes Intestinal Development Through Modulation of Gut Microbiota in Weaning Piglets – Tianwei Wang – Frontiers in Microbiology

Water microbiome and extremophiles

Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities – Cresten Mansfeldt – ISME Journal

Microbial community structure and functionality in the deep sea floor: evaluating the causes of spatial heterogeneity in a submarine canyon system (NW Mediterranean, Spain) – Sara Román – Frontiers in Marine Science

Non-microbiology picks

Dual AAV-mediated gene therapy restores hearing in a DFNB9 mouse model – Omar Akil – PNAS

 

December 20, 2018

In the wait of Christmas weekend and holidays, some quick reading for updates in microbiome field. Today’s digest include articles on improving metagenomic data analysis and integrating different -omics datasets; review article on potential of microbiome to address antimicrobial resistance and meta-analysis on benefits of probiotic supplements in kidney disease.

General microbiome

Microbiome as a tool and a target in the effort to address antimicrobial resistance – David A. Relman – PNAS

Gut microbiota and health: connecting actors across the metabolic system – F. Fava – Proceedings of the Nutrition Society

Dietary sugar silences a colonization factor in a mammalian gut symbiont – Guy E. Townsend II – PNAS

Human gut microbiome

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life – Tommi Vatanen – Nature Microbiology

Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota – Bálint Kintses – Nature Microbiology

Fecal Microbiota Transplantation for the Critically Ill Patient – Berkeley N. Limketkai – Nutrition in Clinical Practice

Effects of probiotic supplements on the progression of chronic kidney disease: a meta‐analysis – Sibei Tao – Nephrology

Signatures within the esophageal microbiome are associated with host genetics, age, and disease – Nandan P. Deshpande – Microbiome

Human oral microbiome

Oral microbiomes in children with asthma and dental caries – Sergey V. Cherkasov – Oral Diseases

Animal experiments

Microbial fermentation of flaxseed fibers modulates the transcriptome of GPR41-expressing enteroendocrine cells and protects mice against diet-induced obesity – Tulika Arora – Americal Journal of Physiology Endocrinology and Metabolism

Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome – Xiaoyun Wang – Cell Research

Antidepressant treatment modulates the gut microbiome and metabolome during pregnancy and lactation in rats with a depressive-like phenotype – Anouschka S. Ramsteijn – BioRxiv

Association of gut microbiota composition and function with a senescence-accelerated mouse model of Alzheimer’s Disease using 16S rRNA gene and metagenomic sequencing analysis – Weijun Peng – Aging

Prebiotics and synbiotics – in ovo delivery for improved lifespan condition in chicken – M. Siwek – BMC Veterinary Research

The response of colonic mucosa-associated microbiota composition, mucosal immune homeostasis, and barrier function to early-life galactooligosaccharides intervention in suckling piglets – Jue Wang – Journal of Agricultural and Food Chemistry

Techniques

Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis – Michael H. Schwartz – Nature Communications

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data – Nicole M. Davis – Microbiome

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy – Mohammad Sajjad Ghaemi – Bioinformatics

Introducing THOR, a model microbiome for genetic dissection of community behavior – Gabriel L. Lozano – BioRxiv

Microbes in the news

Prebiotics Benefit the Gut Microbiome of Both Children and Adults – Market watch

Non-microbiology picks

Technologies to address antimicrobial resistance – Stephen J. Baker – PNAS

December 19, 2018

Toady’s digest features research that gives insight on the formation of lower respiratory tract microbiota in infants and the differential role of TL1A in acute and chronic colitis.

General microbiome

Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease – Steven A. Cowman – PLOS ONE


Pregnancy and early life

*Early-Life Formation of the Microbial and Immunological Environment of the Human Airways – CélinePattaroni – Cell Host & Microbe


Human reproductive microbiome

Review: Uterine microbiome—low biomass and high expectations – Iolanda Garcia-Grau – Biology of Reproduction


Human respiratory microbiome

Review: Microbiome and disease in the upper airway – Jivianne T. Lee – Current Opinion in Allergy and Clinical Immunology


Human gut microbiome

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa – Cormac Brian Fitzgerald – BMC Genomics

Retrospective analysis of long-term gastrointestinal symptoms after Clostridium difficile infection in a nonelderly cohort – Tamar F. Barlam – PLOS ONE

Review: Gut microbiota: a potential manipulator for host adipose tissue and energy metabolism – Bohan Rong – The Journal of Nutritional Biochemistry


Animal experiments

*Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis – Jim G.Castellanos – Immunity

LC–MS-Based Metabolomics and Lipidomics Study of High-Density-Lipoprotein-Modulated Glucose Metabolism with an apoA-I Knockout Mouse Model – Jia Liu – Journal of Proteome Research

TLR4 deficiency reduces pulmonary resistance to Streptococcus pneumoniae in gut microbiota-disrupted mice – Hongyan Wang – PLOS ONE

Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats – Deliang Liu – Biomedicine & Pharmacotherapy


Animal microbiome

Floral and Foliar Source Affect the Bee Nest Microbial Community – Jason A. Rothman – Microbial Ecology

Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus – Matthew Fuirst – PLOS ONE

Disruption of the microbiota affects physiological and evolutionary aspects of insecticide resistance in the German cockroach, an important urban pest – Jose E. Pietri _ PLOS ONE

The composition and structure of the intestinal microflora of Anguilla marmorata at different growth rates: a deep sequencing study – Mao Lin – Journal of Applied Microbiology

Review: Composition and functional roles of the gut microbiota in mosquitoes – Michael R. Strand – Current Opinion in Insect Science

Review: Transcriptomic analyses uncover emerging roles of mucins, lysosome/secretory addressing and detoxification pathways in insect midguts – Walter R. Terra – Current Opinion in Insect Science

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals – Amanda C. Perofsky – The ISME Journal


Plant, root, and soil microbiome

Dead or alive; or does it really matter? Level of congruency between trophic modes in total and active fungal communities in High Arctic soil – Magdalena Wutkowska – Frontiers in Microbiology


Water and extremophile microbiome

Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities – Alberto Scoma- The ISME Journal

Evidence of selective pressure in whale fall microbiome proteins and its potential application to industry – Robert Cardoso deFreitas – Marine Genomics

AgNPs change microbial community structures of wastewater – Yuting Guo – Frontiers in Microbiology

Performance and microbial community of an electric biological integration reactor (EBIR) for treatment of wastewater containing ibuprofen – Yan Feng – Bioresource Technology

 

Food microbiology

Spoilage microbial community profiling by 16S rRNA amplicon sequencing of modified atmosphere packaged live mussels at cold storage temperature – Olumide A.Odeyemi – Food Research International

Genomic resolution of bacterial populations in saccharin and cyclamate degradation – YuDeng – Science of The Total Environment


Phages and viruses

Nanopore-based detection and characterization of yam viruses – Denis Filloux – Scientific Reports


Metabolomics

Active Acupoints Differ from Inactive Acupoints in Modulating Key Plasmatic Metabolites of Hypertension: A Targeted Metabolomics Study – Mingxiao Yang – Scientific Reports


Techniques

Review: Quantifying microbial chatter: scanning electrochemical microscopy as a tool to study interactions in biofilms – Sophie E. Darch – Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences

Metabolic Fingerprinting of Bacteria Exposed to Nanomaterials, Using Online Databases, NMR, and High-Resolution Mass Spectrometry – Theodoros G. Chatzimitakos – Nanotoxicity

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Science, publishing, and career

Commentary : Communicating health risks in science publications: time for everyone to take responsibility – Alexandra L. J. Freeman – BMC Medicine

Could a double blind peer review process reduce gender bias?

Preprint: The Case For and Against Double-blind Reviews – Amelia R – bioRxiv